I agree 100% with what you've said here but what Neil is talking about isn't the disease itself but the act of 'choosing' what gender the disease affects.
Let's break it down even further.
Let's Steelman his argument.
A ) Say the concept is that a disease was created on purpose to infect just women. Indeed, these evil fictional biochemists would potentially qualify as misogynists.
But the concept itself wouldn't necessarily be misogynist, because depiction is not endorsement. If portrayal means endorsement, then Neil has far bigger problems on his hands and he needs to take a frank look at Naught Dog's back catalogue, ridden with violence against women. He hasn't disavow Naughty Dog's past work, has he?
B ) Alternatively, let's say the concept is that the disease is entirely natural and not engineered and that it infects only one sex by pure bad luck. In what way would picking women express hatred for them? Would choosing men instead express misandry?
Does picking one of the sexes as the universal victim in a dystopian fictional setting in a video game necessarily entail hatred towards the real-life members of that sex? Why?
I can think of several creative reasons why choosing women would potentially make for a more interesting scenario. One of them is the very basic fact that women give birth and would perhaps pass down the disease. The stakes would be so much higher: the possible extinction of mankind.
So imagine the indictment he is casting on his own team and on himself. The concept was motivated by hatred for women. This is so extreme and so at odds with his decision not to fire anyone that I think you framed it perfectly. This sounds like atonement, like expiation for sins committed by men against women. The implicit assumption is that any choice that can be perceived as unfavourable to women, even binary choices in the realm of fiction, can
only be ascribed to misogyny. Men are culturally misogynous. That's the implicit assumption. It's not that himself or his team is particularly bad. It's the air. It's the zeitgeist that renders men misogynist by default.
So Neil isn't really talking about the concept or the process and decision that led up to it. No. He is pointing the finger at men in general. It's all vicarious, He isn't condemning the concept - his reference to Feminist Frequency strongly supports this assertion. But men in general, across time, up until this miraculous day of epiphany, that is, when Anita Sarkesian showed him the light and he decided to redeem masculinity by himself.